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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,171 +1,171 @@ | ||
| ## Loading Nonmem Files #### | ||
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| ## FUNCTION LOAD CTL #### | ||
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| #' Load NONMEM ctl file into R | ||
| #' | ||
| #' Loads the NONMEM ctl file into R for translation to mrgsolve format. | ||
| #' | ||
| #' @param filename String of the NONMEM model name without the .ctl extension | ||
| #' @param dir String of the directory path to the NONMEM run files | ||
| #' | ||
| #' @return R dataframe of the NONMEM ctl file | ||
| #' | ||
| #' @examples | ||
| #' load_ctl(filename = "nonmem-model", dir = "path/to/directory/") | ||
| #' | ||
| #' @export | ||
| load_ctl <- function(filename = NULL, dir = ""){ | ||
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| ctl <- read.delim2(paste0(dir,filename,".ctl"), header = F) %>% | ||
| dplyr::mutate(V1 = trimws(V1, which = "both"))%>% # remove leading and trailing white space | ||
| dplyr::filter(substr(V1,1,1) != ";", V1 != "")%>% # remove white space or comment rows | ||
| dplyr::mutate(V1 = gsub(";.*","",V1))%>% # remove anything after comment | ||
| dplyr::mutate(FLG_BLOCK = ifelse(startsWith(V1, "$"), 1, 0))%>% # flag beginning of each block | ||
| dplyr::mutate(BLOCK = suppressWarnings(ifelse(FLG_BLOCK == 1, trimws(substr(V1,2,6), which = "both"), NA)))%>% # get block name | ||
| dplyr::mutate(BLOCK = zoo::na.locf(BLOCK, na.rm = F, fromLast = F)) # pull block name down until next block starts | ||
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| return(ctl) | ||
| } | ||
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| ## FUNCTION LOAD EXT #### | ||
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| #' Load NONMEM ext file into R | ||
| #' | ||
| #' Loads the NONMEM ext file into R for capture of the final estimates. | ||
| #' | ||
| #' @param filename String of the NONMEM model name without the .ext extension | ||
| #' @param dir String of the directory path to the NONMEM run files | ||
| #' @param sigdig Numeric of the number of significant digits to round non-fixed thetas and etas to; -1 for no rounding | ||
| #' @param use.cnv Logical for whether to use the NONMEM cnv file for final parameter estimates instead of the ext file (\code{T} or \code{F}) | ||
| #' | ||
| #' @return R list of the NONMEM final OFV, parameter estimates, and IIV magnitudes | ||
| #' | ||
| #' @examples | ||
| #' load_ext(filename = "nonmem-model", dir = "path/to/directory/") | ||
| #' | ||
| #' @export | ||
| load_ext <- function(filename = NULL, dir = "", sigdig = -1, use.cnv = F){ | ||
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| ext00 <- read.table(paste0(dir,filename,".ext"),sep='',header=T,fill=T,na.strings=".", skip=1) | ||
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| if(class(ext00$ITERATION) != "numeric"){ | ||
| for(i in 1:ncol(ext00)){ | ||
| ext00[,i] <- as.numeric(ext00[,i]) | ||
| } | ||
| rm(i) | ||
| } | ||
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| if(use.cnv == T){ | ||
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| ext0 <- read.table(paste0(dir,filename,".cnv"),sep='',header=T,fill=T,na.strings =".",skip=1)%>% | ||
| dplyr::filter(ITERATION == -2000000000) | ||
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| }else{ | ||
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| ext0 <- ext00 %>% | ||
| dplyr::filter(ITERATION == -1000000000) %>% # NONMEM User Guide VIII for definition (final estimates) | ||
| dplyr::filter(dplyr::row_number() == max(dplyr::row_number())) | ||
| } | ||
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| tmpfixed <- ext00 %>% | ||
| dplyr::filter(ITERATION == -1000000006) %>% # NONMEM User Guide VIII for definition (fixed parameters) | ||
| dplyr::filter(dplyr::row_number() == max(dplyr::row_number())) | ||
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| if(sigdig > 0){ | ||
| omnofix <- tmpfixed[1,dplyr::starts_with("OMEGA", vars = colnames(tmpfixed))] | ||
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| if(class(omnofix)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| omnofix <- data.frame("OMEGA.1.1." = omnofix) | ||
| } | ||
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| omnofix <- colnames(omnofix[which(omnofix[1,] != 1)]) | ||
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| if(length(omnofix)>0){ # 3/17/2024 fix load when all IIV fixed | ||
| tmpomnofix <- lapply(1:length(omnofix), function(i){ | ||
| nofixtmpa <- strsplit(trimws(omnofix[[i]]),"\\.") | ||
| return(data.frame(R = as.numeric(nofixtmpa[[1]][2]), C = as.numeric(nofixtmpa[[1]][3]))) | ||
| }) | ||
| omnofix <- dplyr::bind_rows(tmpomnofix) | ||
| }else{ | ||
| omnofix <- NULL | ||
| } | ||
| }else{ | ||
| omnofix <- NULL | ||
| } | ||
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| ext <- list(NITER = NA, OFV = NA, THETA = NA, OMEGA = NA) | ||
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| ext$NITER <- max(ext00$ITERATION) | ||
| ext$OFV <- ext0[1,which(substr(colnames(ext0),nchar(colnames(ext0))-2,nchar(ext0)) == "OBJ")] | ||
| ext$THETA <- ext0[1,dplyr::starts_with("THETA",vars = colnames(ext0))] | ||
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| tmpom0 <- ext0[1,dplyr::starts_with("OMEGA",vars = colnames(ext0))] | ||
| if(class(tmpom0)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| tmpom0 <- data.frame("OMEGA.1.1." = tmpom0) | ||
| } | ||
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| tmpn <- strsplit(trimws(colnames(tmpom0)[ncol(tmpom0)]), "\\.") | ||
| tmpn <- as.numeric(tmpn[[1]][length(tmpn[[1]])]) | ||
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| tmpom2 <- matrix(data = 0, ncol = tmpn, nrow = tmpn) | ||
| colnames(tmpom2) <- paste0("OMEGA",1:tmpn) | ||
| rownames(tmpom2) <- paste0("OMEGA",1:tmpn) | ||
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| tmpom <- tmpom0[1, which(tmpom0 != 0)] | ||
| if(class(tmpom)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| tmpom_val <- tmpom | ||
| tmpom <- data.frame() | ||
| tmpom[1,colnames(tmpom0)[which(tmpom0!=0)]] = tmpom_val | ||
| } | ||
|
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| if(length(tmpom)>0){ # 3/17/2024 fix error all IIV fixed to zero | ||
| for(i in 1:length(tmpom)){ | ||
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| tmp <- strsplit(trimws(colnames(tmpom)[i]),"\\.")[[1]] | ||
| tmpr <- as.numeric(tmp[2]) | ||
| tmpc <- as.numeric(tmp[3]) | ||
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| if(sigdig > 0 & !is.null(omnofix)){ # 3/17/2024 fix load when all iiv fixed | ||
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| omvalround <- tmpom[1,i] | ||
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| tmpa <- which(omnofix$R == tmpr) | ||
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| if(length(tmpa)>0){ | ||
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| tmpa <- omnofix[tmpa,] | ||
| tmpa <- which(tmpa$C == tmpc) | ||
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| if(length(tmpa)>0){ | ||
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| omvalround <- signif(tmpom[1,i], sigdig) | ||
| } | ||
| } | ||
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| tmpom2[tmpr,tmpc] <- omvalround | ||
| tmpom2[tmpc,tmpr] <- omvalround | ||
|
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| }else{ | ||
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| tmpom2[tmpr,tmpc] <- tmpom[1,i] | ||
| tmpom2[tmpc,tmpr] <- tmpom[1,i] | ||
| } | ||
| } | ||
| } | ||
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| ext$OMEGA <- tmpom2 | ||
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| if(sigdig > 0){ | ||
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| thnofix <- which(tmpfixed[1,dplyr::starts_with("THETA",vars = colnames(tmpfixed))] != 1) | ||
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| if(length(thnofix)>0){ | ||
| ext[["THETA"]][thnofix] <- signif(ext[["THETA"]][thnofix],sigdig) | ||
| } | ||
| } | ||
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| return(list(ext=ext,ext0=ext0)) | ||
| } | ||
|
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| ## END #### | ||
| ## Loading Nonmem Files #### | ||
|
|
||
| ## FUNCTION LOAD CTL #### | ||
|
|
||
| #' Load NONMEM ctl file into R | ||
| #' | ||
| #' Loads the NONMEM ctl file into R for translation to mrgsolve format. | ||
| #' | ||
| #' @param filename String of the NONMEM model name without the .ctl extension | ||
| #' @param dir String of the directory path to the NONMEM run files | ||
| #' | ||
| #' @return R dataframe of the NONMEM ctl file | ||
| #' | ||
| #' @examples | ||
| #' # load_ctl(filename = "nonmem-model", dir = "path/to/directory/") | ||
| #' | ||
| #' @export | ||
| load_ctl <- function(filename = NULL, dir = ""){ | ||
|
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| ctl <- read.delim2(paste0(dir,filename,".ctl"), header = F) %>% | ||
| dplyr::mutate(V1 = trimws(V1, which = "both"))%>% # remove leading and trailing white space | ||
| dplyr::filter(substr(V1,1,1) != ";", V1 != "")%>% # remove white space or comment rows | ||
| dplyr::mutate(V1 = gsub(";.*","",V1))%>% # remove anything after comment | ||
| dplyr::mutate(FLG_BLOCK = ifelse(startsWith(V1, "$"), 1, 0))%>% # flag beginning of each block | ||
| dplyr::mutate(BLOCK = suppressWarnings(ifelse(FLG_BLOCK == 1, trimws(substr(V1,2,6), which = "both"), NA)))%>% # get block name | ||
| dplyr::mutate(BLOCK = zoo::na.locf(BLOCK, na.rm = F, fromLast = F)) # pull block name down until next block starts | ||
|
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| return(ctl) | ||
| } | ||
|
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| ## FUNCTION LOAD EXT #### | ||
|
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||
| #' Load NONMEM ext file into R | ||
| #' | ||
| #' Loads the NONMEM ext file into R for capture of the final estimates. | ||
| #' | ||
| #' @param filename String of the NONMEM model name without the .ext extension | ||
| #' @param dir String of the directory path to the NONMEM run files | ||
| #' @param sigdig Numeric of the number of significant digits to round non-fixed thetas and etas to; -1 for no rounding | ||
| #' @param use.cnv Logical for whether to use the NONMEM cnv file for final parameter estimates instead of the ext file (\code{T} or \code{F}) | ||
| #' | ||
| #' @return R list of the NONMEM final OFV, parameter estimates, and IIV magnitudes | ||
| #' | ||
| #' @examples | ||
| #' load_ext(filename = "nonmem-model", dir = "path/to/directory/") | ||
| #' | ||
| #' @export | ||
| load_ext <- function(filename = NULL, dir = "", sigdig = -1, use.cnv = F){ | ||
|
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| ext00 <- read.table(paste0(dir,filename,".ext"),sep='',header=T,fill=T,na.strings=".", skip=1) | ||
|
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| if(class(ext00$ITERATION) != "numeric"){ | ||
| for(i in 1:ncol(ext00)){ | ||
| ext00[,i] <- as.numeric(ext00[,i]) | ||
| } | ||
| rm(i) | ||
| } | ||
|
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| if(use.cnv == T){ | ||
|
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| ext0 <- read.table(paste0(dir,filename,".cnv"),sep='',header=T,fill=T,na.strings =".",skip=1)%>% | ||
| dplyr::filter(ITERATION == -2000000000) | ||
|
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| }else{ | ||
|
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| ext0 <- ext00 %>% | ||
| dplyr::filter(ITERATION == -1000000000) %>% # NONMEM User Guide VIII for definition (final estimates) | ||
| dplyr::filter(dplyr::row_number() == max(dplyr::row_number())) | ||
| } | ||
|
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| tmpfixed <- ext00 %>% | ||
| dplyr::filter(ITERATION == -1000000006) %>% # NONMEM User Guide VIII for definition (fixed parameters) | ||
| dplyr::filter(dplyr::row_number() == max(dplyr::row_number())) | ||
|
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| if(sigdig > 0){ | ||
| omnofix <- tmpfixed[1,dplyr::starts_with("OMEGA", vars = colnames(tmpfixed))] | ||
|
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| if(class(omnofix)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| omnofix <- data.frame("OMEGA.1.1." = omnofix) | ||
| } | ||
|
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| omnofix <- colnames(omnofix[which(omnofix[1,] != 1)]) | ||
|
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| if(length(omnofix)>0){ # 3/17/2024 fix load when all IIV fixed | ||
| tmpomnofix <- lapply(1:length(omnofix), function(i){ | ||
| nofixtmpa <- strsplit(trimws(omnofix[[i]]),"\\.") | ||
| return(data.frame(R = as.numeric(nofixtmpa[[1]][2]), C = as.numeric(nofixtmpa[[1]][3]))) | ||
| }) | ||
| omnofix <- dplyr::bind_rows(tmpomnofix) | ||
| }else{ | ||
| omnofix <- NULL | ||
| } | ||
| }else{ | ||
| omnofix <- NULL | ||
| } | ||
|
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| ext <- list(NITER = NA, OFV = NA, THETA = NA, OMEGA = NA) | ||
|
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| ext$NITER <- max(ext00$ITERATION) | ||
| ext$OFV <- ext0[1,which(substr(colnames(ext0),nchar(colnames(ext0))-2,nchar(ext0)) == "OBJ")] | ||
| ext$THETA <- ext0[1,dplyr::starts_with("THETA",vars = colnames(ext0))] | ||
|
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| tmpom0 <- ext0[1,dplyr::starts_with("OMEGA",vars = colnames(ext0))] | ||
| if(class(tmpom0)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| tmpom0 <- data.frame("OMEGA.1.1." = tmpom0) | ||
| } | ||
|
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| tmpn <- strsplit(trimws(colnames(tmpom0)[ncol(tmpom0)]), "\\.") | ||
| tmpn <- as.numeric(tmpn[[1]][length(tmpn[[1]])]) | ||
|
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| tmpom2 <- matrix(data = 0, ncol = tmpn, nrow = tmpn) | ||
| colnames(tmpom2) <- paste0("OMEGA",1:tmpn) | ||
| rownames(tmpom2) <- paste0("OMEGA",1:tmpn) | ||
|
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| tmpom <- tmpom0[1, which(tmpom0 != 0)] | ||
| if(class(tmpom)=="numeric"){ # 3/17/2024 fix load when only 1 IIV | ||
| tmpom_val <- tmpom | ||
| tmpom <- data.frame() | ||
| tmpom[1,colnames(tmpom0)[which(tmpom0!=0)]] = tmpom_val | ||
| } | ||
|
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| if(length(tmpom)>0){ # 3/17/2024 fix error all IIV fixed to zero | ||
| for(i in 1:length(tmpom)){ | ||
|
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| tmp <- strsplit(trimws(colnames(tmpom)[i]),"\\.")[[1]] | ||
| tmpr <- as.numeric(tmp[2]) | ||
| tmpc <- as.numeric(tmp[3]) | ||
|
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| if(sigdig > 0 & !is.null(omnofix)){ # 3/17/2024 fix load when all iiv fixed | ||
|
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| omvalround <- tmpom[1,i] | ||
|
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| tmpa <- which(omnofix$R == tmpr) | ||
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| if(length(tmpa)>0){ | ||
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| tmpa <- omnofix[tmpa,] | ||
| tmpa <- which(tmpa$C == tmpc) | ||
|
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| if(length(tmpa)>0){ | ||
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| omvalround <- signif(tmpom[1,i], sigdig) | ||
| } | ||
| } | ||
|
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| tmpom2[tmpr,tmpc] <- omvalround | ||
| tmpom2[tmpc,tmpr] <- omvalround | ||
|
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| }else{ | ||
|
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| tmpom2[tmpr,tmpc] <- tmpom[1,i] | ||
| tmpom2[tmpc,tmpr] <- tmpom[1,i] | ||
| } | ||
| } | ||
| } | ||
|
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| ext$OMEGA <- tmpom2 | ||
|
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| if(sigdig > 0){ | ||
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| thnofix <- which(tmpfixed[1,dplyr::starts_with("THETA",vars = colnames(tmpfixed))] != 1) | ||
|
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| if(length(thnofix)>0){ | ||
| ext[["THETA"]][thnofix] <- signif(ext[["THETA"]][thnofix],sigdig) | ||
| } | ||
| } | ||
|
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| return(list(ext=ext,ext0=ext0)) | ||
| } | ||
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| ## END #### |
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